Mercurial > repos > nick > allele_counts
comparison tests/artificial-samples.vcf.in @ 5:31361191d2d2
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Version 1.1: Stranded output, slightly different handling of minor allele ties and 0 coverage sites, revised help text, added test datasets.
| author | nick |
|---|---|
| date | Thu, 12 Sep 2013 11:34:23 -0400 |
| parents | |
| children |
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| 4:898eb3daab43 | 5:31361191d2d2 |
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| 1 ##fileformat=VCFv4.1 | |
| 2 ##comment="ARGS=-f 10 -c 10" | |
| 3 ##comment="This is a test set of made-up sites, in this case to test the handling of multiple read groups. It's meant to be run with -f 10 -c 10" | |
| 4 ##fileDate=19700101 | |
| 5 ##source=Dan | |
| 6 ##reference=file:///scratch/dan/galaxy/galaxy-central/database/files/002/dataset_0000.dat | |
| 7 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed"> | |
| 8 ##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed"> | |
| 9 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> | |
| 10 ##FORMAT=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed"> | |
| 11 ##FORMAT=<ID=AF,Number=.,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed"> | |
| 12 ##FORMAT=<ID=NC,Number=.,Type=String,Description="Nucleotide and indel counts"> | |
| 13 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT BRAIN ARTERY THYROID | |
| 14 # naive case | |
| 15 chr1 0 . A G,C . . AC=;AF= GT:AC:AF:NC 0/0:1:1:+A=15,-A=15, 0/0:1:1:+G=15,-G=15, 0/0:1:1:+C=15,-C=15, | |
| 16 # cases all with one allele, but different minor allele numbers below threshold | |
| 17 chr1 10 . A G . . AC=;AF= GT:AC:AF:NC 0/0:1:1:+A=15,-A=15, 0/0:1:1:+A=15,+G=1,-A=15,-G=1, 0/0:1:1:+A=15,+G=1,-A=16, | |
| 18 # cases with different numbers of alleles | |
| 19 chr1 20 . A G . . AC=;AF= GT:AC:AF:NC 0/0:1:1:+A=15,+G=1,-A=15,-G=1, 0/0:1:1:+A=17,+G=3,-A=17,-G=3, 0/0:1:1:+A=15,+G=2,-A=15, | |
| 20 # cases where some shouldn't be printed | |
| 21 chr1 30 . A G . . AC=;AF= GT:AC:AF:NC 0/0:1:1:+A=15,-A=15, 0/0:1:1:+A=9,-A=8, 0/0:1:1:+A=15,-A=9, | |
| 22 # cases with some complex pre-':' data | |
| 23 chr1 40 . T A,G,C . . AC=1,1;AF=0.0111111111111,0.0111111111111 GT:AC:AF:NC 0/0:1:1:+T=15,-T=15, 0/0:1,1:0.0111111111111,0.0111111111111:+A=1,+T=81,-T=16,-G=2, 0/0:3,1:0.0394736842105,0.0131578947368:+C=52,+T=30,-C=17,-T=1, |